Re: [Open Babel] InChIs, CML, OpenBabel 3D generation - what's going on?

[Noel O'Boyle <baoilleach@gm...>]

Hello Flo,

Over the last two months Tim Vandermeesch has rewritten the stereo
handling code in OpenBabel. Stereo flipping will be a thing of the
past with OB 2.3. You can try the latest from his or my Git repository
on github. I've just ported the InChI code but not yet CML.

- Noel

2009/4/30  <flo-ml@...>:
> Hi all,
>
> I played around with InChIs for a bit and only got more and more confused
> the more I did. As far as I know, they are there to make things easier, and
> I hoped that would be the case. But no.
>
> You may wonder what that has to do with OpenBabel, and that's a valid
> question. (It has to do with using OpenBabel to get the correct input format
> for the Standard InChI software v1.2.)
>
> I wrote up a post on my blog that I'm not going to reproduce here. Please
> have a look and be intrigued.
>
> http://flo.nigsch.com/?p=67
>
> I'm really looking forward to any comments on that.
>
> Best,
>
> Flo
>
>
>

[Open Babel] InChIs, CML, OpenBabel 3D generation - what's going on?

[<flo-ml@ni...>]

Hi all,

I played around with InChIs for a bit and only got more and more  
confused the more I did. As far as I know, they are there to make  
things easier, and I hoped that would be the case. But no.

You may wonder what that has to do with OpenBabel, and that's a valid  
question. (It has to do with using OpenBabel to get the correct input  
format for the Standard InChI software v1.2.)

I wrote up a post on my blog that I'm not going to reproduce here.  
Please have a look and be intrigued.

http://flo.nigsch.com/?p=67

I'm really looking forward to any comments on that.

Best,

Flo

Re: [Open Babel] bond length and bondangle determin by openbable.....

[Xavier Prat-Resina <xavier.prat.resina@gm...>]

I forgot to mention that if you are only intersted in bonds
there's a bondIter
<--
import pybel, openbabel

mol = pybel.readfile("mol","nf3_3d.mol").next()
for atom in mol:
    a = atom.OBAtom
    for obbond in openbabel.OBAtomBondIter(a):
        print obbond.GetLength()
-->

Xavier

On Thu, Apr 30, 2009 at 6:46 AM, Xavier Prat-Resina <
xavier.prat.resina@...> wrote:

> Hi Kulbir,
>
> to compute bond distances I use the openbabel libraries from python.
>
> <--
> import pybel
>
> mol = pybel.readfile("mol","nf3_3d.mol").next()
> i=0
> for atom in mol:
>     for coor in mol.atoms[i].coords:
>         print coor
>     i+=1
> --->
>
> with the atomic coordinates you can compute any distance you want.
> I don't know if there's any better way.
>
> Cheers
>
> Xavier
>
> On Wed, Apr 29, 2009 at 1:22 AM, Kulbir Kaur <kulbir28@...> wrote:
>
>>  Hi,
>> I am a new comer in using openbabel. There are couple of questions:
>> (1) Can I use openbable for finding bondlength and bondangle of thousands
>> of atoms?
>> (2) The bond angles and bondlengths in mopin format are of nearest
>> neighbour atoms  in a sample having thousands of atom?
>>  Thanks,
>> Kulbir,
>> Research Scholar,
>> Panab University,
>> Chandigarh.
>>
>> ------------------------------
>> Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition
>> * Click here!<http://in.rd.yahoo.com/tagline_firefox_1/*http://downloads.yahoo.com/in/firefox/>;
>>
>>
>> ------------------------------------------------------------------------------
>> Register Now & Save for Velocity, the Web Performance & Operations
>> Conference from O'Reilly Media. Velocity features a full day of
>> expert-led, hands-on workshops and two days of sessions from industry
>> leaders in dedicated Performance & Operations tracks. Use code vel09scf
>> and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>
>
> --
> Xavier Prat-Resina
> Research Associate
> Journal of Chemical Education and University of Wisconsin
> 209 N. Brooks St. Madison, WI  53715-1116
>
> Tel: 608 8901702 // Fax: 608 2627145
> e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat
> http://x.prat.resina.googlepages.com
>



-- 
Xavier Prat-Resina
Research Associate
Journal of Chemical Education and University of Wisconsin
209 N. Brooks St. Madison, WI  53715-1116

Tel: 608 8901702 // Fax: 608 2627145
e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com

Re: [Open Babel] bond length and bondangle determin by openbable.....

[Xavier Prat-Resina <xavier.prat.resina@gm...>]

Hi Kulbir,

to compute bond distances I use the openbabel libraries from python.

<--
import pybel

mol = pybel.readfile("mol","nf3_3d.mol").next()
i=0
for atom in mol:
    for coor in mol.atoms[i].coords:
        print coor
    i+=1
--->

with the atomic coordinates you can compute any distance you want.
I don't know if there's any better way.

Cheers

Xavier

On Wed, Apr 29, 2009 at 1:22 AM, Kulbir Kaur <kulbir28@...> wrote:

> Hi,
> I am a new comer in using openbabel. There are couple of questions:
> (1) Can I use openbable for finding bondlength and bondangle of thousands
> of atoms?
> (2) The bond angles and bondlengths in mopin format are of nearest
> neighbour atoms  in a sample having thousands of atom?
>  Thanks,
> Kulbir,
> Research Scholar,
> Panab University,
> Chandigarh.
>
> ------------------------------
> Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition
> * Click here!<http://in.rd.yahoo.com/tagline_firefox_1/*http://downloads.yahoo.com/in/firefox/>;
>
>
> ------------------------------------------------------------------------------
> Register Now & Save for Velocity, the Web Performance & Operations
> Conference from O'Reilly Media. Velocity features a full day of
> expert-led, hands-on workshops and two days of sessions from industry
> leaders in dedicated Performance & Operations tracks. Use code vel09scf
> and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>


-- 
Xavier Prat-Resina
Research Associate
Journal of Chemical Education and University of Wisconsin
209 N. Brooks St. Madison, WI  53715-1116

Tel: 608 8901702 // Fax: 608 2627145
e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com

[Open Babel] bond length and bondangle determin by openbable.....

[Kulbir Kaur <kulbir28@ya...>]

Hi,
I am a new comer in using openbabel. There are couple of questions:
(1) Can I use openbable for finding bondlength and bondangle of thousands of atoms?
(2) The bond angles and bondlengths in mopin format are of nearest neighbour atoms  in a sample having thousands of atom? 
 Thanks,
Kulbir,
Research Scholar,
Panab University,
Chandigarh.
 


      Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com

Re: [Open Babel] Change /usr/local/share/openbabel

[Noel O'Boyle <baoilleach@gm...>]

I don't know the answer to the original question, but if you set
BABEL_DATADIR to the location of the text files, the command should
work.

- Noel

2009/4/28 Fredrik Wallner <fredrik@...>:
> I mean the text files. The format files in /usr/local/lib/openbabel
> are all available, but when I try to calculate a fingerprint the
> command fingerprint = OBFingerprint::FindFingerprint("FP2"); returns
> NULL.
>
> Regards,
> Fredrik
> 27 apr 2009 kl. 20.12 skrev Geoffrey Hutchison:
>
>>
>> On Apr 27, 2009, at 9:43 AM, Fredrik Wallner wrote:
>>
>>> I am wondering if there is a configuration option in cmake to use a
>>> different dir than /usr/local/share/openbabel for plugin-related
>>> files.
>>
>> Do you mean /usr/local/lib/openbabel? Or do you mean the text files
>> (e.g., elements.txt, etc.)
>>
>> Thanks,
>> -Geoff
>
>
> ------------------------------------------------------------------------------
> Register Now & Save for Velocity, the Web Performance & Operations
> Conference from O'Reilly Media. Velocity features a full day of
> expert-led, hands-on workshops and two days of sessions from industry
> leaders in dedicated Performance & Operations tracks. Use code vel09scf
> and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

Re: [Open Babel] Change /usr/local/share/openbabel

[Fredrik Wallner <fredrik@wa...>]

I mean the text files. The format files in /usr/local/lib/openbabel  
are all available, but when I try to calculate a fingerprint the  
command fingerprint = OBFingerprint::FindFingerprint("FP2"); returns  
NULL.

Regards,
Fredrik
27 apr 2009 kl. 20.12 skrev Geoffrey Hutchison:

>
> On Apr 27, 2009, at 9:43 AM, Fredrik Wallner wrote:
>
>> I am wondering if there is a configuration option in cmake to use a
>> different dir than /usr/local/share/openbabel for plugin-related
>> files.
>
> Do you mean /usr/local/lib/openbabel? Or do you mean the text files  
> (e.g., elements.txt, etc.)
>
> Thanks,
> -Geoff

Re: [Open Babel] Change /usr/local/share/openbabel

[Geoffrey Hutchison <geoff@ge...>]

On Apr 27, 2009, at 9:43 AM, Fredrik Wallner wrote:

> I am wondering if there is a configuration option in cmake to use a
> different dir than /usr/local/share/openbabel for plugin-related
> files.

Do you mean /usr/local/lib/openbabel? Or do you mean the text files  
(e.g., elements.txt, etc.)

Thanks,
-Geoff

Re: [Open Babel] openbabel

[Noel O'Boyle <baoilleach@gm...>]

See A4 in the installation instructions at
http://openbabel.org/wiki/Install_(source_code). Your LD_LIBRARY_PATH
should point to the location of libopenbabel.so, probably
/usr/local/lib in your case.

- Noel

2009/4/24 hwttdz <joseph.bylund@...>:
>
> I'm having the same error, I did not choose a prefix for configure, i.e.
> ./configure
> I did run make install and I have a binary in
> /usr/local/bin/babel
> however on execution I get
> "/usr/local/bin/babel: error while loading shared libraries:
> libopenbabel.so.3: cannot open shared object file: No such file or
> directory"
> I tried setting LD_LIBRARY_PATH to /usr/local/lib/openbabel/2.2.1, before
> execution, but it doesn't seem to have helped (and the library doesn't exist
> in that directory).
>
>
>
> Igor Filippov [Contr] wrote:
>>
>> What prefix did you choose for configure?
>> Did you run "make install"?
>> Did you set up LD_LIBRARY_PATH variable accordingly?
>>
>> Igor
>>
>>
>> On Fri, 2009-03-06 at 13:19 +0000, Kamel Mansouri wrote:
>>>         hello every body,
>>>         i'm trying to use openbabel to convert files from different
>>>         formats, but i didn't found any binary file for 32 byte i386,
>>>         so i compiled the sources, but still not able to run the
>>>         program because of an unfound library and im getting this
>>>         error message:
>>>         babel: error while loading shared libraries:
>>>         libopenbabel.so.1: cannot open shared object file: No such
>>>         file or directory
>>>
>>>         if some one already have a binary file or can give solution
>>>         with this library,please help!!
>>>         thanx
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@...
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>
> --
> View this message in context: http://www.nabble.com/openbabel-tp22435007p23219510.html
> Sent from the openbabel-discuss mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Crystal Reports &#45; New Free Runtime and 30 Day Trial
> Check out the new simplified licensign option that enables unlimited
> royalty&#45;free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

[Open Babel] Change /usr/local/share/openbabel

[Fredrik Wallner <fredrik@wa...>]

Hi!

I am wondering if there is a configuration option in cmake to use a  
different dir than /usr/local/share/openbabel for plugin-related  
files. I believe I have a problem with newer versions of MySQL where  
the stuff in the mentioned directory can't be accessed.

Kind regards,
Fredrik

Re: [Open Babel] Scripting Child Process

[Jack Shultz <jshultz@hy...>]

I got it figured out. I just need to put it all in the first string of
the array. Probably more a perl question than a Babel. Thanks for the
help.
@args = ("/usr/local/bin/babel /usr/local/NCI/PLATED.sdf -omol2
".$count.".mol2 --filter \"title='".$count."'\"");

Jack

On Mon, Apr 27, 2009 at 4:23 AM, Noel O'Boyle <baoilleach@...> wrote:
> I don't know anything about Perl (so can't help), but you may want to use
> the OpenBabel Perl bindings directly here. You can implement the filter by
> having a loop where you test the title.
>
> - Noel
>
> 2009/4/26 Jack Shultz <jshultz@...>
>>
>> Hello,
>>
>> I'm working on a perl script to extract files and submit them for
>> analysis. Initially I was using a back tick, but now I think we need
>> to create a child process so the parent waits. The way I am trying to
>> do that is with system function.
>>
>> I have a counter in a for loop that goes through the list of ligands
>> ....
>> @args = ("/usr/local/bin/babel", " -isdf", "
>> /usr/local/NCI/PLATED.sdf", " -omol2", "
>> /home/boincadm/drugdiscovery/ligand.mol2", " --filter
>> \"title='".$count."'\"");
>> $args = join('', @args);
>> print $args . "\n";
>> #$ligand = join('', @ligand);
>> system(@args) == 0
>>        or die "system @args failed: $?";
>>
>> Here is the error
>>
>> [boincadm@... drugdiscovery]$ ./nci_fork_autodock.pl
>> /usr/local/bin/babel -isdf /usr/local/NCI/PLATED.sdf -omol2
>> /home/boincadm/drugdiscovery/ligand.mol2 --filter "title='1'"
>> babel: cannot write output format!
>> Open Babel 2.2.1 -- Apr 21 2009 -- 19:39:23
>> Usage: babel [-i<input-type>] <name> [-o<output-type>] <name>
>> Try  -H option for more information.
>> child exited with value 0
>>
>>
>> --
>> Jack
>>
>> http://www.facebook.com/home.php#/profile.php?id=832713248
>> http://hydrogenathome.org
>>
>>
>> ------------------------------------------------------------------------------
>> Crystal Reports &#45; New Free Runtime and 30 Day Trial
>> Check out the new simplified licensign option that enables unlimited
>> royalty&#45;free distribution of the report engine for externally facing
>> server and web deployment.
>> http://p.sf.net/sfu/businessobjects
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>



-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org

Re: [Open Babel] Scripting Child Process

[Noel O'Boyle <baoilleach@gm...>]

I don't know anything about Perl (so can't help), but you may want to use
the OpenBabel Perl bindings directly here. You can implement the filter by
having a loop where you test the title.

- Noel

2009/4/26 Jack Shultz <jshultz@...>

> Hello,
>
> I'm working on a perl script to extract files and submit them for
> analysis. Initially I was using a back tick, but now I think we need
> to create a child process so the parent waits. The way I am trying to
> do that is with system function.
>
> I have a counter in a for loop that goes through the list of ligands
> ....
> @args = ("/usr/local/bin/babel", " -isdf", "
> /usr/local/NCI/PLATED.sdf", " -omol2", "
> /home/boincadm/drugdiscovery/ligand.mol2", " --filter
> \"title='".$count."'\"");
> $args = join('', @args);
> print $args . "\n";
> #$ligand = join('', @ligand);
> system(@args) == 0
>        or die "system @args failed: $?";
>
> Here is the error
>
> [boincadm@... drugdiscovery]$ ./nci_fork_autodock.pl
> /usr/local/bin/babel -isdf /usr/local/NCI/PLATED.sdf -omol2
> /home/boincadm/drugdiscovery/ligand.mol2 --filter "title='1'"
> babel: cannot write output format!
> Open Babel 2.2.1 -- Apr 21 2009 -- 19:39:23
> Usage: babel [-i<input-type>] <name> [-o<output-type>] <name>
> Try  -H option for more information.
> child exited with value 0
>
>
> --
> Jack
>
> http://www.facebook.com/home.php#/profile.php?id=832713248
> http://hydrogenathome.org
>
>
> ------------------------------------------------------------------------------
> Crystal Reports &#45; New Free Runtime and 30 Day Trial
> Check out the new simplified licensign option that enables unlimited
> royalty&#45;free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

[Open Babel] Scripting Child Process

[Jack Shultz <jshultz@hy...>]

Hello,

I'm working on a perl script to extract files and submit them for
analysis. Initially I was using a back tick, but now I think we need
to create a child process so the parent waits. The way I am trying to
do that is with system function.

I have a counter in a for loop that goes through the list of ligands
....
@args = ("/usr/local/bin/babel", " -isdf", "
/usr/local/NCI/PLATED.sdf", " -omol2", "
/home/boincadm/drugdiscovery/ligand.mol2", " --filter
\"title='".$count."'\"");
$args = join('', @args);
print $args . "\n";
#$ligand = join('', @ligand);
system(@args) == 0
        or die "system @args failed: $?";

Here is the error

[boincadm@... drugdiscovery]$ ./nci_fork_autodock.pl
/usr/local/bin/babel -isdf /usr/local/NCI/PLATED.sdf -omol2
/home/boincadm/drugdiscovery/ligand.mol2 --filter "title='1'"
babel: cannot write output format!
Open Babel 2.2.1 -- Apr 21 2009 -- 19:39:23
Usage: babel [-i<input-type>] <name> [-o<output-type>] <name>
Try  -H option for more information.
child exited with value 0


-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org

Re: [Open Babel] OBMolAngleIter() wrong angles?

[Iordan Hristov <hristov@uc...>]

>>> The answer probably is a redundant set of all internal bond angles  
>>> e.g. 6 angles for CH4. (The current result is actually no angles)
>>
>> I'm open to expanding methods to a redundant set, but the current  
>> code generates angle terms for force fields -- in which case,  
>> redundancy is not necessarily welcome.
>>
>> I'm not sure why methane would generate no angles. I would normally  
>> expect three angles. I'll have to set up a test.
>>
>> -Geoff
>
> If the forcefield implements a "H-C-H" bending potential for CH4  
> it's likely it uses the redundant set of angles. I think forcefields  
> that don't use such a set would screen the redundant angles based on  
> the atom names, say have a H1-C-H2 bending potential entry but not a  
> H1-C-H4 entry. Maybe OBMolAngleIter() and OBMolTorsionIter() could  
> have the default redundant behavior (as it's determined by  
> connectivity alone) and take an optional forcefield argument that  
> would chop off the redundant (for that forcefield) angles.
>
> Iordan

I just tested methane (as [H]C([H])([H])[H]) with OpenBabel 2-2-1 and  
it actually reports all angles, including redundant ones:

bonds [(1, 2), (2, 3), (2, 4), (2, 5)]
angles [(1, 0, 2), (1, 0, 3), (1, 0, 4), (1, 2, 3), (1, 2, 4), (1, 3,  
4)]

So all is good!

Iordan

Re: [Open Babel] Some errors in obiter.h.

[Geoffrey Hutchison <geoff@ge...>]

> But now I'm teaching C++ and I think it's good idea to start real  
> world project.

How about a good 2D molecular editor? ;-) Avogadro has also had a few  
real-world student projects as enhancements. In any case, welcome to  
the community.

> The only bad thing is that there is no information about it nowhere  
> at official web site. I think it's unexpected behavior and someone  
> should mention this point in wiki or/and on API description pages.

No, "unexpected behavior" is a bug and the header should be fixed.  
It's now fixed in the 2.2 branch for 2.2.2 and the SVN trunk for 2.3.

Thanks!
-Geoff

Re: [Open Babel] Some errors in obiter.h.

[Anton Simakov <kemiisto@gm...>]

Hi, Tim.
Hi, Geoff.
Thanks for your help!

Hmm. Out of curiosity, what are you working on?


Don't worry! I now about Avogadro. =) I'm trying to make something like this
great program. May be it's good idea to add some functionality to
Avogadro... But now I'm teaching C++ and I think it's good idea to start
real world project. And also for me it's much more simpler and interesting
to start from scratch.

Well, you're right, the obiter.h header has some errors -- it should do more
> forward declarations. But that's because most people do something like:
>
> #include <openbabel/mol.h>
> #include <openbabel/obiter.h>
>
> That should work.


The only bad thing is that there is no information about it nowhere at
official web site. I think it's unexpected behavior and someone should
mention this point in wiki or/and on API description pages.

Best regards,
Anton

Re: [Open Babel] OBMolAngleIter() wrong angles?

[Iordan Hristov <hristov@uc...>]

> Well, I'll grant that the user may expect angles similar to a set of  
> internal coordinates -- e.g., start at the first atom, then one  
> neighbor, then the next. But I don't think the current code is all  
> that unexpected -- start with the first atom as the vertex, generate  
> angles around that, then move to the second atom, etc.
>

This will look more consistent with the way OBMolTorsionIter() reports  
the torsions.

>> The answer probably is a redundant set of all internal bond angles  
>> e.g. 6 angles for CH4. (The current result is actually no angles)
>
> I'm open to expanding methods to a redundant set, but the current  
> code generates angle terms for force fields -- in which case,  
> redundancy is not necessarily welcome.
>
> I'm not sure why methane would generate no angles. I would normally  
> expect three angles. I'll have to set up a test.
>
> -Geoff

If the forcefield implements a "H-C-H" bending potential for CH4 it's  
likely it uses the redundant set of angles. I think forcefields that  
don't use such a set would screen the redundant angles based on the  
atom names, say have a H1-C-H2 bending potential entry but not a H1-C- 
H4 entry. Maybe OBMolAngleIter() and OBMolTorsionIter() could have the  
default redundant behavior (as it's determined by connectivity alone)  
and take an optional forcefield argument that would chop off the  
redundant (for that forcefield) angles.

Iordan

Re: [Open Babel] openbabel

[hwttdz <joseph.bylund@gm...>]

I'm having the same error, I did not choose a prefix for configure, i.e.
./configure
I did run make install and I have a binary in 
/usr/local/bin/babel
however on execution I get 
"/usr/local/bin/babel: error while loading shared libraries:
libopenbabel.so.3: cannot open shared object file: No such file or
directory"
I tried setting LD_LIBRARY_PATH to /usr/local/lib/openbabel/2.2.1, before
execution, but it doesn't seem to have helped (and the library doesn't exist
in that directory).  



Igor Filippov [Contr] wrote:
> 
> What prefix did you choose for configure?
> Did you run "make install"?
> Did you set up LD_LIBRARY_PATH variable accordingly?
> 
> Igor
> 
> 
> On Fri, 2009-03-06 at 13:19 +0000, Kamel Mansouri wrote:
>>         hello every body,
>>         i'm trying to use openbabel to convert files from different
>>         formats, but i didn't found any binary file for 32 byte i386,
>>         so i compiled the sources, but still not able to run the
>>         program because of an unfound library and im getting this
>>         error message: 
>>         babel: error while loading shared libraries:
>>         libopenbabel.so.1: cannot open shared object file: No such
>>         file or directory
>>         
>>         if some one already have a binary file or can give solution
>>         with this library,please help!! 
>>         thanx
>>         
>>         
>>         
>>         
>> 
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> 
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> 
> 

-- 
View this message in context: http://www.nabble.com/openbabel-tp22435007p23219510.html
Sent from the openbabel-discuss mailing list archive at Nabble.com.

Re: [Open Babel] OBMolAngleIter() wrong angles?

[Geoffrey Hutchison <geoff@ge...>]

On Apr 24, 2009, at 4:14 AM, Noel O'Boyle wrote:

> The question is what set of angles does the user expect?

Well, I'll grant that the user may expect angles similar to a set of  
internal coordinates -- e.g., start at the first atom, then one  
neighbor, then the next. But I don't think the current code is all  
that unexpected -- start with the first atom as the vertex, generate  
angles around that, then move to the second atom, etc.

> The answer probably is a redundant set of all internal bond angles  
> e.g. 6 angles for CH4. (The current result is actually no angles)

I'm open to expanding methods to a redundant set, but the current code  
generates angle terms for force fields -- in which case, redundancy is  
not necessarily welcome.

I'm not sure why methane would generate no angles. I would normally  
expect three angles. I'll have to set up a test.

-Geoff

Re: [Open Babel] OBMolAngleIter() wrong angles?

[Noel O'Boyle <baoilleach@gm...>]

The question is what set of angles does the user expect? The answer probably
is a redundant set of all internal bond angles e.g. 6 angles for CH4. (The
current result is actually no angles)

If a definitive set of angles cannot be agreed then this function may be of
little use to others. Perhaps it would be better simply to point users to
the GetAngle() method of OBAngle so that they can calculate the angles
themselves.

- Noel

2009/4/23 Tim Vandermeersch <tim.vandermeersch@...>

> On Thu, Apr 23, 2009 at 11:35 PM, Iordan Hristov <hristov@...>
> wrote:
> > The Open Babel "FindAngles" method doesn't work like you're expecting.
> > Instead, it starts at the first atom (0 in Pybel notation) and looks for
> two
> > neighbors.
> >
> > If that was the case in H-O-O-H we would get the correct angle sequence
> > H-O-O but we get O-H-O for the first angle.
>
> O-H-O is correct using the previously described notation as far as I
> can see. The first O is the angle corner and the H and O are the
> terminals. (note: O-H-O does not imply the hydrogen has two bonded
> atoms!)
>
> > Instead, you seem to be expecting that it finds the first atom, then goes
> to
> > a neighbor, and then to the next.
> >
> > Well, I think people who will use the iterator would expect nothing more
> or
> > less than the angles that actually appear in their molecules. As it is
> right
> > now we get some mangled version of the angles with the atoms permuted. If
> > the intent of OBMolAngleIter() was to return a  sequence of atoms that
> form
> > an angle only when rearranged that should be noted in the documentation.
> But
> > why should the method rearrange the sequences it finds and not return
> them
> > in the correct order (like H-O-O)? That must be a bug.
>
> The angles are actually found in this order. We iterate over all
> atoms, iterate over their neighbor atoms and add the angles to the
> list.
>
> Tim
>
> > Thanks,
> > Iordan
> >
> > On Apr 23, 2009, at 10:43 AM, Geoffrey Hutchison wrote:
> >
> > angles [(1, 0, 2), (2, 1, 3)]
> >
> > ...
> >
> > One would expect to get the angles as (0,1,2) and (1,2,3) so what's going
> > on? I'm using OpenBabel 2-2-1 compiled from svn.
> >
> > The Open Babel "FindAngles" method doesn't work like you're expecting.
> > Instead, it starts at the first atom (0 in Pybel notation) and looks for
> two
> > neighbors. Instead, you seem to be expecting that it finds the first
> atom,
> > then goes to a neighbor, and then to the next.
> >
> > The does seem to be some interest in using the ordering you mention.
> Other
> > opinions from the list?
> >
> > Cheers,
> > -Geoff
> >
> >
> > Hello,
> > when I build a hydrogen peroxide from SMILES I get a wrong angle
> > sequence (while the bonds and dihedral are ok).
> > Here is the output for the molecule (H-O-O-H):
> > mass [1.0079400000000001, 15.9994, 15.9994, 1.0079400000000001]
> > bonds [(1, 2), (2, 3), (3, 4)]
> > angles [(1, 0, 2), (2, 1, 3)]
> > dihedral [(0, 1, 2, 3)]
> > One would expect to get the angles as (0,1,2) and (1,2,3) so what's going
> > on? I'm using OpenBabel 2-2-1 compiled from svn.
> > Thanks,
> > Iordan
> >
> > p.s. the Python script:
> > import openbabel
> > obConversion = openbabel.OBConversion()
> > obConversion.SetInAndOutFormats("smi", "mdl")
> > mol = openbabel.OBMol()
> > obConversion.ReadString(mol,"[H]OO[H]")
> > print 'mass', [i.GetAtomicMass() for i in openbabel.OBMolAtomIter(mol)]
> > print 'bonds',
> >
> [(i.GetBeginAtomIdx(),i.GetEndAtomIdx()) for i in openbabel.OBMolBondIter(mol)]
> > print 'angles', [i for i in openbabel.OBMolAngleIter(mol)]
> > print 'dihedral', [i for i in openbabel.OBMolTorsionIter(mol)]
> >
> >
> ------------------------------------------------------------------------------
> > Crystal Reports &#45; New Free Runtime and 30 Day Trial
> > Check out the new simplified licensign option that enables unlimited
> > royalty&#45;free distribution of the report engine for externally facing
> > server and web deployment.
> > http://p.sf.net/sfu/businessobjects
> > _______________________________________________
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
> >
>
>
> ------------------------------------------------------------------------------
> Crystal Reports &#45; New Free Runtime and 30 Day Trial
> Check out the new simplified licensign option that enables unlimited
> royalty&#45;free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

Re: [Open Babel] Some errors in obiter.h.

[Geoffrey Hutchison <geoff@ge...>]

> I try to use OpenBabel in my Qt app.

Hmm. Out of curiosity, what are you working on?

> When i include <openbabel/obiter.h> I get some error messages:

Well, you're right, the obiter.h header has some errors -- it should  
do more forward declarations. But that's because most people do  
something like:

#include <openbabel/mol.h>
#include <openbabel/obiter.h>

That should work.

Cheers,
-Geoff

Re: [Open Babel] OBMolAngleIter() wrong angles?

[Tim Vandermeersch <tim.vandermeersch@gm...>]

On Thu, Apr 23, 2009 at 11:35 PM, Iordan Hristov <hristov@...> wrote:
> The Open Babel "FindAngles" method doesn't work like you're expecting.
> Instead, it starts at the first atom (0 in Pybel notation) and looks for two
> neighbors.
>
> If that was the case in H-O-O-H we would get the correct angle sequence
> H-O-O but we get O-H-O for the first angle.

O-H-O is correct using the previously described notation as far as I
can see. The first O is the angle corner and the H and O are the
terminals. (note: O-H-O does not imply the hydrogen has two bonded
atoms!)

> Instead, you seem to be expecting that it finds the first atom, then goes to
> a neighbor, and then to the next.
>
> Well, I think people who will use the iterator would expect nothing more or
> less than the angles that actually appear in their molecules. As it is right
> now we get some mangled version of the angles with the atoms permuted. If
> the intent of OBMolAngleIter() was to return a  sequence of atoms that form
> an angle only when rearranged that should be noted in the documentation. But
> why should the method rearrange the sequences it finds and not return them
> in the correct order (like H-O-O)? That must be a bug.

The angles are actually found in this order. We iterate over all
atoms, iterate over their neighbor atoms and add the angles to the
list.

Tim

> Thanks,
> Iordan
>
> On Apr 23, 2009, at 10:43 AM, Geoffrey Hutchison wrote:
>
> angles [(1, 0, 2), (2, 1, 3)]
>
> ...
>
> One would expect to get the angles as (0,1,2) and (1,2,3) so what's going
> on? I'm using OpenBabel 2-2-1 compiled from svn.
>
> The Open Babel "FindAngles" method doesn't work like you're expecting.
> Instead, it starts at the first atom (0 in Pybel notation) and looks for two
> neighbors. Instead, you seem to be expecting that it finds the first atom,
> then goes to a neighbor, and then to the next.
>
> The does seem to be some interest in using the ordering you mention. Other
> opinions from the list?
>
> Cheers,
> -Geoff
>
>
> Hello,
> when I build a hydrogen peroxide from SMILES I get a wrong angle
> sequence (while the bonds and dihedral are ok).
> Here is the output for the molecule (H-O-O-H):
> mass [1.0079400000000001, 15.9994, 15.9994, 1.0079400000000001]
> bonds [(1, 2), (2, 3), (3, 4)]
> angles [(1, 0, 2), (2, 1, 3)]
> dihedral [(0, 1, 2, 3)]
> One would expect to get the angles as (0,1,2) and (1,2,3) so what's going
> on? I'm using OpenBabel 2-2-1 compiled from svn.
> Thanks,
> Iordan
>
> p.s. the Python script:
> import openbabel
> obConversion = openbabel.OBConversion()
> obConversion.SetInAndOutFormats("smi", "mdl")
> mol = openbabel.OBMol()
> obConversion.ReadString(mol,"[H]OO[H]")
> print 'mass', [i.GetAtomicMass() for i in openbabel.OBMolAtomIter(mol)]
> print 'bonds',
> [(i.GetBeginAtomIdx(),i.GetEndAtomIdx()) for i in openbabel.OBMolBondIter(mol)]
> print 'angles', [i for i in openbabel.OBMolAngleIter(mol)]
> print 'dihedral', [i for i in openbabel.OBMolTorsionIter(mol)]
>
> ------------------------------------------------------------------------------
> Crystal Reports &#45; New Free Runtime and 30 Day Trial
> Check out the new simplified licensign option that enables unlimited
> royalty&#45;free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>

Re: [Open Babel] OBMolAngleIter() wrong angles?

[Iordan Hristov <hristov@uc...>]

> The Open Babel "FindAngles" method doesn't work like you're  
> expecting. Instead, it starts at the first atom (0 in Pybel  
> notation) and looks for two neighbors.

If that was the case in H-O-O-H we would get the correct angle  
sequence H-O-O but we get O-H-O for the first angle.

> Instead, you seem to be expecting that it finds the first atom, then  
> goes to a neighbor, and then to the next.


Well, I think people who will use the iterator would expect nothing  
more or less than the angles that actually appear in their molecules.  
As it is right now we get some mangled version of the angles with the  
atoms permuted. If the intent of OBMolAngleIter() was to return a   
sequence of atoms that form an angle only when rearranged that should  
be noted in the documentation. But why should the method rearrange the  
sequences it finds and not return them in the correct order (like H-O- 
O)? That must be a bug.


Thanks,
Iordan


On Apr 23, 2009, at 10:43 AM, Geoffrey Hutchison wrote:

>> angles [(1, 0, 2), (2, 1, 3)]
> ...
>> One would expect to get the angles as (0,1,2) and (1,2,3) so what's  
>> going on? I'm using OpenBabel 2-2-1 compiled from svn.
>
> The Open Babel "FindAngles" method doesn't work like you're  
> expecting. Instead, it starts at the first atom (0 in Pybel  
> notation) and looks for two neighbors. Instead, you seem to be  
> expecting that it finds the first atom, then goes to a neighbor, and  
> then to the next.
>
> The does seem to be some interest in using the ordering you mention.  
> Other opinions from the list?
>
> Cheers,
> -Geoff
>
>

>> Hello,
>>
>> when I build a hydrogen peroxide from SMILES I get a wrong angle  
>> sequence (while the bonds and dihedral are ok).
>> Here is the output for the molecule (H-O-O-H):
>>
>> mass [1.0079400000000001, 15.9994, 15.9994, 1.0079400000000001]
>> bonds [(1, 2), (2, 3), (3, 4)]
>> angles [(1, 0, 2), (2, 1, 3)]
>> dihedral [(0, 1, 2, 3)]
>>
>> One would expect to get the angles as (0,1,2) and (1,2,3) so what's  
>> going on? I'm using OpenBabel 2-2-1 compiled from svn.
>>
>> Thanks,
>> Iordan
>>
>>
>> p.s. the Python script:
>>
>> import openbabel
>>
>> obConversion = openbabel.OBConversion()
>> obConversion.SetInAndOutFormats("smi", "mdl")
>> mol = openbabel.OBMol()
>> obConversion.ReadString(mol,"[H]OO[H]")
>>
>> print 'mass', [i.GetAtomicMass() for i in  
>> openbabel.OBMolAtomIter(mol)]
>> print 'bonds', [(i.GetBeginAtomIdx(),i.GetEndAtomIdx()) for i in  
>> openbabel.OBMolBondIter(mol)]
>> print 'angles', [i for i in openbabel.OBMolAngleIter(mol)]
>> print 'dihedral', [i for i in openbabel.OBMolTorsionIter(mol)]
>

Re: [Open Babel] OBMolAngleIter() wrong angles?

[Geoffrey Hutchison <geoff@ge...>]

> angles [(1, 0, 2), (2, 1, 3)]
...
> One would expect to get the angles as (0,1,2) and (1,2,3) so what's  
> going on? I'm using OpenBabel 2-2-1 compiled from svn.

The Open Babel "FindAngles" method doesn't work like you're expecting.  
Instead, it starts at the first atom (0 in Pybel notation) and looks  
for two neighbors. Instead, you seem to be expecting that it finds the  
first atom, then goes to a neighbor, and then to the next.

The does seem to be some interest in using the ordering you mention.  
Other opinions from the list?

Cheers,
-Geoff

Re: [Open Babel] Some errors in obiter.h.

[Tim Vandermeersch <tim.vandermeersch@gm...>]

Hi,

The easiest way to solve the problem is just to include
openbabel/mol.h, it includes all headers in the right order.

Tim

On Thu, Apr 23, 2009 at 3:35 PM, Anton Simakov <kemiisto@...> wrote:
> Hello everybody.
>
> I try to use OpenBabel in my Qt app. When i include <openbabel/obiter.h> I
> get some error messages:
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:341: error:
> 'OBRing' was not declared in this scope
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:341: error:
> template argument 1 is invalid
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:341: error:
> template argument 2 is invalid
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:341: error:
> invalid use of '::'
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:341: error:
> expected ';' before '_i'
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:342: error:
> ISO C++ forbids declaration of 'OBRing' with no type
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:342: error:
> expected ';' before '*' token
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:344: error:
> ISO C++ forbids declaration of 'OBRingData' with no type
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:344: error:
> expected ';' before '*' token
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:361: error:
> ISO C++ forbids declaration of 'OBRing' with no type
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:361: error:
> expected ';' before '*' token
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:363: error:
> expected `;' before 'OBRing'
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:363: error:
> ISO C++ forbids declaration of 'OBRing' with no type
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:363: error:
> expected ';' before '&' token
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:364: error:
> expected `;' before '}' token
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h: In
> constructor 'OpenBabel::OBMolRingIter::OBMolRingIter()':
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:347: error:
> class 'OpenBabel::OBMolRingIter' does not have any field named '_ptr'
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:347: error:
> class 'OpenBabel::OBMolRingIter' does not have any field named '_rings'
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h: In member
> function 'OpenBabel::OBMolRingIter::operator bool() const':
> /Users/kemiisto/Downloads/openbabel/include/openbabel/obiter.h:355: error:
> '_ptr' was not declared in this scope
>
> I use Mac OS X 10.5 and have no problems with compiling and installing
> OpenBabel. But something goes wrong with headers...
> I try different versions (2.2.0, 2.2.1, svn).
>
> What's rong?
>
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today.
> Use priority code J9JMT32. http://p.sf.net/sfu/p
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>